Post date: May 09, 2014 3:48:0 PM
Now that the 1986 alignments are complete for the whole genome sequences from the within generation experiment, I am using samtools to merge those for each individual and assign the individual ID, i.e., individual number, and plant-block treatment for the within generation experiment. The results will be in data/timema/timema_wgrs/assembliesExperiment/. Here is an example of the commands submitted via a perl wrapper script:
cd /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/
samtools merge -nr timemaTC_2C_24787.bam aln_4_296*sorted.bam
samtools sort timemaTC_2C_24787.bam timemaTC_2C_24787.sorted
rm -f timemaTC_2C_24787.bam
samtools index timemaTC_2C_24787.sorted.bam